From owner-repertoires@net.bio.net Sun Oct 01 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Australian Peptide Conference Preliminary Announcement Date: 2 Oct 1995 13:17:17 +0100 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <44ol8d$a8k@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk This is a preliminary announcement for the 2nd Australian Peptide Conference "From Discovery to Therapeutics" which will take place next year. Date: October 6th-11th, 1996 Location: Kingfisher Bay, Fraser Island, Queensland, Australia. Contact: Dr. A. Ian Smith Conference Secretary Baker Medical Research Institute P.O. Box 348, Prahran, Victoria 3181 Australia Tel. +61-3-9522-4333 Fax +61-3-9521-1362 (no email) Book early as the number of delegates is limited to 250! Andrew |========================================================================| | Andrew Wallace | Discussion on phage display, | | | combinatorial libraries, etc. - | | IRBM P. Angeletti, | bionet.molecules.repertoires | | Via Pontina KM 30.600 | molreps@daresbury.ac.uk | | 00040 Pomezia, Italy. |-------------------------------------------| | | "It has not escaped our notice that | | Voice: +39-6-91093434 | the specific pairing we have postulated | | Fax: +39-6-91093225 | immediately suggests a possible copying | | Email: wallace@irbm.it | mechanism for the genetic material." | | | | | DISCLAIMER: I do not speak | J.D. Watson and F.H.C. Crick | | on behalf of anyone. | in Nature 171:737-737 (1953). | |========================================================================| From owner-repertoires@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!MACC.WISC.EDU!GOSINK From: GOSINK@MACC.WISC.EDU (Mark Gosink) Newsgroups: bionet.molecules.repertoires Subject: Questions about a meeting and a book. Date: 3 Oct 1995 12:46:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <25100309410497@vms2.macc.wisc.edu> NNTP-Posting-Host: net.bio.net Dear Netters: I have a couple of quick questions. The first is: Has anyone heard of the "Exploiting Molecular Diversity" meeting this January in Coronado, California? Is it any good? The second question is: I wrote a question to the molreps newsgroup a few months ago asking about a book that was to be published on molecular libraries. Unfortunately, I lost the response I received. Does any one know if such a book has been published? I beleive it was supposed to come out about now. Thanks for any responses. Mark ************************************************************************* * Dr. Mark Gosink Post-doctoral Fellow * * Department of Horticulture (608) 262-1622 voice * * University of Wisconsin-Madison (608) 262-4743 FAX * * 1575 Linden Dr. * * Madison ,WI 53706 GOSINK@MACC.WISC.EDU (internet) * ************************************************************************* From owner-repertoires@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Janet Clench, Library, Tel:(39 6)91093220" Newsgroups: bionet.molecules.repertoires Subject: This week's reference update. Ciao! Date: 3 Oct 1995 17:10:33 +0100 Lines: 77 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <44rn9p$rlf@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk *************************************************** SUBJECT: Combinatorial & Phage Libraries DATE: October 2, 1995 *************************************************** Angewandte Chemie - International Edition in English 34: 16 (SEP 1 1995) C Gennari, HP Nestler, B Salom, WC Still Solid-phase synthesis of vinylogous sulfonyl peptides 1763-1765 Angewandte Chemie - International Edition in English 34: 16 (SEP 1 1995) C Gennari, HP Nestler, B Salom, WC Still Synthetic receptors based on vinylogous sulfonyl peptides 1765-1768 Tetrahedron Letters 36: 35 (AUG 28 1995) V Krchnak, Z Flegelova, AS Weichsel, M Lebl Polymer-supported mitsunobu ether formation and its use in combinatorial chemistry 6193-6196 Bioorganic & Medicinal Chemistry Letters 5: 17 (SEP 7 1995) B Neustadt, A Wu, EM Smith, T Nechuta, A Fawzi, H Zhang, AK Ganguly A case study of combinatorial libraries: Endothelin receptor antagonist hexapeptides 2041-2044 Journal of Immunological Methods 184: 2 (AUG 18 1995) RS Ames, MA Tornetta, K Deen, CS Jones, AM Swift, S Ganguly Conversion of murine Fabs isolated from a combinatorial phage display library to full length immunoglobulins 177-186 FEMS Microbiology Reviews 17: 1-2 (AUG 1995) RN Perham, TD Terry, AE Willis, J Greenwood, FD Veronese, E Appella Engineering a peptide epitope display system on filamentous bacteriophage 25-31 FEMS Microbiology Reviews 17: 1-2 (AUG 1995) BH Lindqvist, S Naderi Peptide presentation by bacteriophage P4 33-39 FEMS Microbiology Reviews 17: 1-2 (AUG 1995) RNH Konings, RHA Folmer, PJM Folkers, M Nilges, CW Hilbers Three-dimensional structure of the single-stranded DNA-binding protein encoded by gene V of the filamentous bacteriophage M13 and a model of its complex with single-stranded DNA 57-72 FEMS Microbiology Reviews 17: 1-2 (AUG 1995) A Kuhn Major coat proteins of bacteriophage Pf3 and M13 as model systems for Sec-independent protein transport 185-190 Journal of Molecular Biology 252: 1 (SEP 8 1995) KA Williams, M Glibowicka, ZM Li, H Li, AR Khan, YMY Chen, J Wang, DA Marvin, CM Deber Packing of coat protein amphipathic and transmembrane helices in filamentous bacteriophage M13: Role of small residues in protein oligomerization 6-14 Drug Development Research 35: 4 (AUG 1995) MH Lyttle Combinatorial chemistry: A conservative perspective 230-236 From owner-repertoires@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Re: Questions about a meeting and a book. Date: 4 Oct 1995 12:47:52 +0100 Lines: 44 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <44ts98$ll0@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk In bionet.molecules.repertoires Msg # 20 GOSINK@MACC.WISC.EDU (Mark Gosink) wrote: > >Dear Netters: > I have a couple of quick questions. The first is: Has anyone heard of >the "Exploiting Molecular Diversity" meeting this January in Coronado, >California? Is it any good? Sounds like you mean one of the meetings organised by either IBC or the other crowd (forget their name) which are organising a lot of specialist meetings related to libraries, screening, drug design, etc. I would also like to hear from others what they think about these. I attended one on high-throughput screening last year and found it to be fairly commercial. What do the rest of you think? > The second question is: I wrote a question to the molreps newsgroup >a few months ago asking about a book that was to be published on molecular >libraries. Unfortunately, I lost the response I received. Does any one know if >such a book has been published? I beleive it was supposed to come out about >now. > Thanks for any responses. >Mark Brian Kay was putting together a book like the one you describe, in fact a number of people have been asking about it. Brian, are you out there reading this? What's the story? Andrew |========================================================================| | Andrew Wallace | Discussion on phage display, | | | combinatorial libraries, etc. - | | IRBM P. Angeletti, | bionet.molecules.repertoires | | Via Pontina KM 30.600 | molreps@daresbury.ac.uk | | 00040 Pomezia, Italy. |-------------------------------------------| | | "It has not escaped our notice that | | Voice: +39-6-91093434 | the specific pairing we have postulated | | Fax: +39-6-91093225 | immediately suggests a possible copying | | Email: wallace@irbm.it | mechanism for the genetic material." | | | | | DISCLAIMER: I do not speak | J.D. Watson and F.H.C. Crick | | on behalf of anyone. | in Nature 171:737-737 (1953). | |========================================================================| From owner-repertoires@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: How to subscribe to molreps Date: 4 Oct 1995 18:26:03 +0100 Lines: 194 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <44ug3b$bp7@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk In Message-Id: <9510041412.AA74160@umabnet.ab.umd.edu> pemanuel@umabnet.ab.edu (Peter) wrote: >My newsgroup does not subscribe to this newsgroup. I do have TELNET and >Netscape capability. Is there another way I can gain access to this >newsgroup? > Peter > >-- >Peter Emanuel Ph.D. >University of Maryland School of Medicine >4-027 Bressler Research Building >655 West Baltimore Street >Baltimore, MD 21201 Here is some help for those who may be having trouble getting this group. Andrew ---------------------------MOLECULAR-REPERTOIRES------------------------- Subscribing to this group: -------------------------- IF YOU USE USENET NEWS: you need do nothing other than participate in bionet.molecules.repertoires when it appears in your newsreader. Depending upon your news software, this may entail you having to answer a prompt indicating that you want to subscribe. You might also try the command "g bionet.molecules.repertoires" in rn-like newsreaders. 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Each file is assigned a date such as 9312 for December 1993. Please note that ours is a UNIX system and all file and directory names are case-sensitive, i.e., upper case file names are different from lower case names. You can also access these same files via Gopher if you start a gopher session using net.bio.net as your gopher server. Gopher also allows you to view the individual messages within each monthly archive file. The files are in the MOLECULAR-REPERTOIRES directory. Postings to bionet.molecules.repertoires are also WAIS indexed and can be searched via either gopher or WAIS at our site. In gopher the option at net.bio.net is "Search Bionet USENET Articles" and in WAIS one should use the WAIS source biosci.src. This is a WAIS index of all BIOSCI/bionet messages including this newsgroup. Please see the BIOSCI FAQ for details. The FAQ can be requested from biosci-help@net.bio.net. Once again, if you have any administrative questions that require personal assistance, please address them to biosci-help@net.bio.net in the U.S. or biosci@daresbury.ac.uk in the UK. Best wishes for a successful newsgroup! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-repertoires@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!lhc.nlm.nih.gov!darwin.sura.net!news.dfn.de!scsing.switch.ch!news.belwue.de!news.uni-mannheim.de!thorin!news.gni.net!news.omnilink.net!news.maz.net!dish.news.pipex.net!pipex!lade.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!howland.reston.ans.net!news.sprintlink.net!news00.sunet.se!sunic!sunic!sunic.sunet.se!columba.udac.uu.se!image.bmc.uu.se!user From: msz@bio.embnet.se (Michael Szardenings) Newsgroups: bionet.molecules.repertoires Subject: lac-supression in pHen and pComb3 Date: Fri, 06 Oct 1995 17:37:23 +0100 Organization: Uppsala University, BMC, Farm.Farm. Lines: 36 Message-ID: NNTP-Posting-Host: image.bmc.uu.se Hi, I am trying to construct a phage display vector for test purposes with the peptide ligand of a receptor. test because I first wanted to establish binding conditions etc for the presumably 'active' (i.e. binding) phage. Because the work is planned to deal also with relatively long peptides, I decided to start of with phagemids. I got 2 derivatives of pHEN and pCOMB3 and tried to ligate the oligonucleotide into these vectors without any success. The oligonucleotide is made up by filling in 2 partially complementary sequences with T4 (Vent in PCR-block worked as well) and digesting them with SmaI and XhoI respectively BamHI. 7% PAGE shows, that the oligonucleotide is filled in and cut correctly. Vectors have been prepared with the same enzymes and treated with AP and they show a relatively low background. The only clones isolated from both plasmids are free from insert or contained parts of the oligonucleotide out of frame. The later vanished, when I improved design of the oligos. SO FINALLY THE QUESTION: I assume that the leaky lac-constructs of the above plasmids lead to some kind of counterselection. Is there anything I can do? I have been using glucose in the mini-preps, but on the plates it had no effect at all. Thanks a lot Michael ========================================================================= * * ****** ******** ********************************************* ** ** *** ** ******** * Michael Szardenings * *** *** ***** *** * Biomedical Center, Pharm. Pharm. * **** **** ***** *** * Box 591 Tel.:int46-18-17422* ** *** ** ** *** ******** * S-751 24 Uppsala FAX :int46-18-55971* ** * ** ****** ******** ********************************************* ========================================================================= INTERNET : MSZ@bmc.uu.se ========================================================================= From owner-repertoires@net.bio.net Fri Oct 06 23:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!in1.uu.net!news1.digital.com!nntp-hub2.barrnet.net!news.Stanford.EDU!oncology-fp-dynamic-201.stanford.edu!user From: renschle@cmgm.stanford.edu (Markus Renschler) Newsgroups: bionet.molecules.repertoires Subject: Re: Combinatorial Peptide Libraries Book Date: Tue, 03 Oct 1995 13:34:37 -0800 Organization: Stanford University Lines: 10 Message-ID: NNTP-Posting-Host: oncology-fp-dynamic-201.stanford.edu To answer Mark Gosink's second question: There is a peptide library book coming out soon by Humana Press, Totowa, NJ (201) 256-1699, edited by Shmuel Cabilly in their Methods in Moecular Biology series of manuals. It will have methods for the generation of synthetic libraries, phage libraries, oligonucleotide encoded libraries, peptide on plasmid libraries, polysome libraries, and application chapters using those libraries. I don't know the exact publication date. Markus Renschler Stanford University e-mail renschle@cmgm.stanford.edu From owner-repertoires@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molecules.repertoires Subject: Re: Combinatorial Peptide Libraries Book Date: 9 Oct 1995 11:19:06 +0100 Lines: 18 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <45asuq$dn4@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk >To answer Mark Gosink's second question: >There is a peptide library book coming out soon by Humana Press, Totowa, >NJ (201) 256-1699, edited by Shmuel Cabilly in their Methods in Moecular >Biology series of manuals. It will have methods for the generation of >synthetic libraries, phage libraries, oligonucleotide encoded libraries, >peptide on plasmid libraries, polysome libraries, and application chapters >using those libraries. I don't know the exact publication date. >Markus Renschler >Stanford University >e-mail renschle@cmgm.stanford.edu Please note that also Methods in Enzymology, Academic Press, (407-345-2000, FAX 407-345-4058) is going to publish a volume on: "Combinatorial Libraries: Preparation, Screening, Selection and Evolution", Edited by John N. Abelson. I still don't know the exact publication date. Franco Felici, IRBM e-mail felici@irbm.it From owner-repertoires@net.bio.net Mon Oct 09 23:00:00 1995 Path: biosci!corp.wrgrace.com!James.A.Braatz From: James.A.Braatz@corp.wrgrace.com Newsgroups: bionet.molecules.repertoires Subject: ChemDiverse software Date: 10 Oct 1995 13:08:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Does anyone have any experience with ChemDiverse, the combinatorial chemistry package from Chemical Design, Inc.? What platform does it run on? What is the approximate cost? Is it any good? Thanks, Jim Braatz From owner-repertoires@net.bio.net Sat Oct 14 23:00:00 1995 Newsgroups: bionet.molecules.repertoires,bionet.info-theory Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!info.uah.edu!maze.dpo.uab.edu!darwin.sura.net!fconvx.ncifcrf.gov!kaylor!toms From: toms@kaylor.ncifcrf.gov (Tom Schneider) Subject: Consensus Sequences: Just Say No! Message-ID: Summary: Data Display for Repertoires Keywords: consensus sequences, sequence logo Sender: usenet@ncifcrf.gov (C News) Nntp-Posting-Host: kaylor.ncifcrf.gov Organization: Frederick Biomedical Supercomputer Center X-Newsreader: TIN [version 1.2 PL2] Date: Sun, 8 Oct 1995 21:16:44 GMT Lines: 25 Xref: biosci bionet.molecules.repertoires:27 bionet.info-theory:3645 If you have created and sequenced a molecular repertoire, you may want to create a summary, and you might do this by making a consensus sequence. Consensus sequences are being used to characterize the binding sites of macromolecules on DNA and RNA. After aligning a set of binding site sequences, the most frequent base is chosen. A position which contains 100% A's will be represented by an A, while a position that is only 75% A will also be represented by an A. The consensus is frequently used to search for binding sites, and the number of mismatches to the consensus is counted. A mismatch to a 100% A position is much more severe than one to a 75% A, but this is not accounted for so the researcher is mislead. Having spent so much trouble to create your data set, you have thrown most of it out by making a consensus. A mathematically robust replacement for the consensus sequence is called the sequence logo. Further information and examples may be found on the internet at http://www-lmmb.ncifcrf.gov/~toms/. Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov http://www-lmmb.ncifcrf.gov/~toms/ From owner-repertoires@net.bio.net Sun Oct 15 23:00:00 1995 Path: biosci!lhc.nlm.nih.gov!crick.ser.bbnplanet.net!lamarck.sura.net!newsfeed.internetmci.com!news.sprintlink.net!simtel!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!daresbury!not-for-mail Newsgroups: bionet.molecules.repertoires Subject: ... and now, a 2 week update for your delight and perusal! Ciao Message-ID: <45u42q$hst@mserv1.dl.ac.uk> From: "Janet Clench, Library, Tel:(39 6)91093220" Date: 16 Oct 1995 18:17:14 +0100 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Original-To: molreps@dl.ac.uk Lines: 64 *************************************************** SUBJECT: Combinatorial & Phage Libraries DATE: October 9, 16, 1995 *************************************************** Tetrahedron Letters 36: 37 (SEP 11 1995) P Kocis, O Issakova, NF Sepetov, M Lebl Kemp's triacid scaffolding for synthesis of combinatorial nonpeptide uncoded libraries 6623-6626 Current Opinion in Structural Biology 5: 4 (AUG 1995) KT Oneil, RH Hoess Phage display: Protein engineering by directed evolution 443-449 Biochemical Society Transactions 23: 3 (AUG 1995) P Walden, KH Wiesmuller, G Jung Elucidation of T-cell epitopes: A synthetic approach with random peptide libraries 678-681 European Journal of Biochemistry 232: 2 (SEP 1 1995) CHM Papavoine, JMA Aelen, RNH Konings, CW Hilbers, FJM Vandeven NMR studies of the major coat protein of bacteriophage M13 - Structural information of gVIIIp in dodecylphosphocholine micelles 490-500 European Journal of Biochemistry 232: 2 (SEP 1 1995) JJ Prompers, RHA Folmer, M Nilges, PJM Folkers, RNH Konings, CW Hilbers Refined solution structure of the Tyr41->His mutant of the M13 gene V protein - A comparison with the crystal structure 506-514 Journal of Biological Chemistry 270: 37 (SEP 15 1995) J Jiracek, A Yiotakis, B Vincent, A Lecoq, A Nicolaou, F Checler, V Dive Development of highly potent and selective phosphinic peptide inhibitors of zinc endopeptidase 24-15 using combinatorial chemistry 21701-21706 Protein Engineering 8: 6 (JUN 1995) K Nord, J Nilsson, B Nilsson, M Uhlen, PA Nygren A combinatorial library of an alpha-helical bacterial receptor domain 601-608 EMBO Journal 14: 17 (SEP 1 1995) RHA Folmer, M Nilges, RNH Konings, CW Hilbers Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: Similarity to other proteins binding to single-stranded nucleic acids 4132-4142 Virus Genes 10: 2 (1995) VP Efimov, IV Nepluev, VV Mesyanzhinov Bacteriophage T4 as a surface display vector 173-177 From owner-repertoires@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Chris.Beard@CibaDiag.COM Newsgroups: bionet.molecules.repertoires Subject: bionet.molecules.repertoires Date: 17 Oct 1995 20:24:45 +0100 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <460vtt$836@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk I saw a post from Andrew Wallace in the bionet.molbio.proteins newsgroup that mentioned bionet.molecules.repertoires as a good place to find information on phage display. Unfortunately this newsgroup does not seem to be available from my Internet provider at this time. Is this a new group that recently formed? Is there a mailing list that can be subscribed to in order to receive the posts to the newsgroup? Thank you. Chris Beard chris.beard@cibadiag.com From owner-repertoires@net.bio.net Mon Oct 16 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: More on sequence logos Date: 17 Oct 1995 12:39:30 +0100 Lines: 44 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4604li$dlj@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk In bionet.molecules.repertoires Msg # 27 toms@kaylor.ncifcrf.gov (Tom Schneider) wrote: >If you have created and sequenced a molecular repertoire, you may want to >create a summary, and you might do this by making a consensus sequence. > [comment on creating consensus sequences deleted] > >Having spent so much trouble to create your data set, you have thrown most of >it out by making a consensus. > >A mathematically robust replacement for the consensus sequence is called the >sequence logo. Further information and examples may be found on the internet >at http://www-lmmb.ncifcrf.gov/~toms/. > Tom Schneider > National Cancer Institute > Laboratory of Mathematical Biology > Frederick, Maryland 21702-1201 > toms@ncifcrf.gov > http://www-lmmb.ncifcrf.gov/~toms/ Sounds interesting, Tom. Would you be prepared to post some of the Web page material here so that those of us without access to a web browser can also take a look? Thanks, Andrew |========================================================================| | Andrew Wallace | Discussion on phage display, | | | combinatorial libraries, etc. - | | IRBM P. Angeletti, | bionet.molecules.repertoires | | Via Pontina KM 30.600 | molreps@daresbury.ac.uk | | 00040 Pomezia, Italy. |-------------------------------------------| | | "It has not escaped our notice that | | Voice: +39-6-91093434 | the specific pairing we have postulated | | Fax: +39-6-91093225 | immediately suggests a possible copying | | Email: wallace@irbm.it | mechanism for the genetic material." | | | | | DISCLAIMER: I do not speak | J.D. Watson and F.H.C. Crick | | on behalf of anyone. | in Nature 171:737-737 (1953). | |========================================================================| From owner-repertoires@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Update on Brian Kay's book Date: 18 Oct 1995 17:33:12 +0100 Lines: 14 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <463a88$980@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk For those asking about Brian's book, here's what he says: >>With regards to the phage display book. It is almost completed. The >>project took longer than I thought due the fact it was a sidelight >>to my typical chaotic life. The editor at Academic Press also >>quit which added more delay. > >I will post to the newgroup a table of contents and expected date of >publication, shortly. > >If anyone wishes more detail, please contact me directly. > >Brian Kay >briankay@email.unc.edu From owner-repertoires@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.molecules.repertoires Subject: RE: Phage titer by OD-measurement? Date: 19 Oct 1995 11:13:58 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4658d6$smi@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk Troels Wind wrote: >About a year back I had a protocol for determining the actual amount of >physical phage particles (M13-like) by spectroscopic measurements, but >I've lost it. So if any of you could send me or guide me to a protocol, >I would appreciate it. physical particles per milliliter = A269 x 6 x 10e16 / genome lenght (in nucleotides) (according to Smith and Scott, Meth. Enzymol. Vol. 217 p. 239) Please note that the above is only reliable for purified (i.e. CsCl gradient) phage preparations. Best wishes, Franco Felici, IRBM From owner-repertoires@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!daresbury!not-for-mail From: Troels Wind Newsgroups: bionet.molecules.repertoires Subject: Phage titer by OD-measurement? Date: 19 Oct 1995 10:24:05 +0100 Lines: 12 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4655fl$q61@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk (molreps) Dear all, About a year back I had a protocol for determining the actual amount of physical phage particles (M13-like) by spectroscopic measurements, but I've lost it. So if any of you could send me or guide me to a protocol, I would appreciate it. Thanks, Troels Wind University of Aarhus Denmark From owner-repertoires@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!CS.Arizona.EDU!uunet!in2.uu.net!newsfeed.internetmci.com!news.sesqui.net!oitnews.harvard.edu!hsph.harvard.edu!lcchen From: Longchuan Chen Newsgroups: bionet.molecules.repertoires Subject: peptoids or peptide library Date: Tue, 17 Oct 1995 15:19:49 -0400 Organization: Harvard University Office of Information Technology Lines: 5 Message-ID: NNTP-Posting-Host: hsph.harvard.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know where I can get combinatorial peptoid libraries for ligand screening purpose? Are they commercially available? Long Chen lcchen@hsph.havard.edu From owner-repertoires@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!ihnp4.ucsd.edu!library.ucla.edu!info.ucla.edu!newsfeed.internetmci.com!news.sprintlink.net!in2.uu.net!newsfeed.pitt.edu!news From: Jacob Burbea Newsgroups: bionet.molecules.repertoires Subject: Re: Phage titer by OD-measurement? Date: 20 Oct 1995 20:58:05 GMT Organization: University of Pitsburgh Lines: 6 Message-ID: <4692gt$fvk@usenet.srv.cis.pitt.edu> References: <4655fl$q61@mserv1.dl.ac.uk> NNTP-Posting-Host: una2.math.pitt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: wind@biobase.dk X-URL: news:4655fl$q61@mserv1.dl.ac.uk Dear Troels, There is a description of spec measurements in the phage-display handbook given by Smith with his distributed libraries. Or see The methods in enzymology article. From owner-repertoires@net.bio.net Tue Oct 24 22:00:00 1995 Newsgroups: bionet.molecules.repertoires Path: biosci!lhc.nlm.nih.gov!crick.ser.bbnplanet.net!lamarck.sura.net!fconvx.ncifcrf.gov!kaylor!toms From: toms@kaylor.ncifcrf.gov (Tom Schneider) Subject: Re: More on sequence logos Message-ID: Sender: usenet@ncifcrf.gov (C News) Nntp-Posting-Host: kaylor.ncifcrf.gov Organization: Frederick Biomedical Supercomputer Center X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 19 Oct 1995 04:02:26 GMT Lines: 50 Andrew Wallace writes: | Sounds interesting, Tom. Would you be prepared to post some of the Web page | material here so that those of us without access to a web browser can also | take a look? Unfortunately that's difficult because the sequence logos are a visual display. They are in PostScript and I have put some in GIF format for the web pages. If you have access to ftp (file transfer protocol) you can look into my archive at ftp.ncifcrf.gov in the directory pub/delila. Some example logos there are: SequenceLogoSculpture.ps (do this one first!) gallery.logo.ps globin.logo.ps hawaii.fig1.ps keller.ps lambcro.logo.ps lexa.logo.ps rbs1055.clist.ps rbs1055.logo.ps ribo.logo.ps splice.cover.ps t7.logo.ps papers: colonsplice.ps hawaii.ps (do this one first!) logopaper.ps (the original paper) malign.ps (multiple alignment) nano2.ps (review) philgen.ps (about databases) primer.ps (teaches info theory) secondlaw.ps sipblurb.ps trieste1995.ps (review) The set of papers we can send to people are listed in: cover.ps If you would like these, email me your physical address. Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov http://www-lmmb.ncifcrf.gov/~toms/ From owner-repertoires@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Re: Antibodies to fd/M13 Needed Date: 26 Oct 1995 18:26:52 -0000 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46ojtc$44c@mserv1.dl.ac.uk> Original-To: peter_prevelige@micro.microbio.uab.edu, molreps@dl.ac.uk Date: Thu, 26 Oct 1995 17:28:54 +0000 (GMT) From: Dennis Prickett To: "Andrew, Tel. +396-91093434" Cc: "bionet.molecules.repertoires mail newsgroup" Subject: Re: Antibodies to fd/M13 Needed In-Reply-To: <95102617110.~INN-LFJa00200.bionet-news@dl.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Pharmacia HRP/Anti-M13 Conjugate 200 plates worth catalogue no. 27-9411-01 Part of the RPAS kit but can be purchased separately > Antibodies to fd/M13 Needed > > Hi all > > We are looking for some polyclonals to fd/M13 to do ELISA assays. The one > commercial source I know of (Accurate Chemical) says that they are > backordered for about a month. Does anyone have some they could spare to > help us out? > From owner-repertoires@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Antibodies to fd/M13 Needed Date: 26 Oct 1995 16:08:39 -0000 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <46obq7$pmu@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk (Reposted by request of Peter Prevelige. Please send replies either to the list or directly to him at the address: peter_prevelige@micro.microbio.uab.edu Thanks. Andrew) Antibodies to fd/M13 Needed Hi all We are looking for some polyclonals to fd/M13 to do ELISA assays. The one commercial source I know of (Accurate Chemical) says that they are backordered for about a month. Does anyone have some they could spare to help us out? Thanks Peter Prevelige Dept. of Microbiology BBRB #416 845 19th Street South Univ. of Alabama at Birmingham Birmingham, AL 35294 205-975-5327 phone 205-975-5479 fax peter_prevelige@micro.microbio.uab.edu From owner-repertoires@net.bio.net Fri Oct 27 22:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molecules.repertoires Subject: IMPORTANT: BIOSCI miniFAQ Date: 28 Oct 1995 02:01:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510280900.CAA23204@net.bio.net> NNTP-Posting-Host: net.bio.net This is a new "miniFAQ" designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the newsgroups from about 95% of the spams that are being sent to date. This means that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. 2) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-repertoires@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +396-91093434" Newsgroups: bionet.molecules.repertoires Subject: Forwarded from bionet.virology Date: 30 Oct 1995 16:40:59 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <472v6r$d4p@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk >From: ijiwaru@wheel.dcn.davis.ca.us >X-Article-Number: bionet.virology Msg # 4765 In article <46lppe$goj@maze.dpo.uab.edu>, Peter Prevelige wrote: > Hi All > > We are looking for polyclonals to fd/M13 since they are backordered from > Accurate Chemical. If anybody has any, or knows of another source, we would > appreciate hearing from you. Thanks > > Peter If I remember correctly, Stratagene has an antibody (can't remember if it is mono or polyclonal) to M13. The Ab might only be against pIII and not to whole phage, but check the catalog. L From owner-repertoires@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!CMGM.STANFORD.EDU!renschle From: renschle@CMGM.STANFORD.EDU (Markus Renschler) Newsgroups: bionet.molecules.repertoires Subject: Anti-M13 antibody Date: 30 Oct 1995 07:01:36 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510261714.KAA14515@cmgm.Stanford.EDU> NNTP-Posting-Host: net.bio.net Pharmacia sells an anti-M13 antibody that is already HRP conjugated and works well in ELISAs, dilute 1:3000 when used as a detector. From owner-repertoires@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!daresbury!not-for-mail From: "Janet Clench, Library, Tel:(39 6)91093220" Newsgroups: bionet.molecules.repertoires Subject: Reference update for the week of October 23. Ciao! Date: 30 Oct 1995 14:28:59 -0000 Lines: 39 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <472nfb$5h3@mserv1.dl.ac.uk> Original-To: molreps@dl.ac.uk *************************************************** SUBJECT: Combinatorial & Phage Libraries DATE: October 23, 1995 *************************************************** Journal of Chromatography A 711: 1 (SEP 8 1995) M Krook, C Lindbladh, S Birnbaum, H Naess, JA Eriksen, K Mosbach Selection of peptides with surface affinity for alpha-chymotrypsin using a phage display library 119-128 Biochemical and Biophysical Research Communications 214: 2 (SEP 14 1995) AS Tanaka, CAM Sampaio, H Fritz, EA Auerswald Functional display and expression of chicken cystatin using a phagemid system 389-395 Biochemistry 34: 37 (SEP 19 1995) WS Sandberg, PM Schlunk, HB Zabin, TC Terwilliger Relationship between in vivo activity and in vitro measures of function and stability of a protein 11970-11978 Peptide Research 8: 4 (JUL-AUG 1995) V Krchnak, AS Weichsel, D Cabel, M Lebl Linear presentation of variable side-chain spacing in a highly diverse combinatorial library 198-205 Proceedings of the National Academy of Sciences of the United States of America 92: 20 (SEP 26 1995) MM Gosink, RD Vierstra Redirecting the specificity of ubiquitination by modifying ubiquitin-conjugating enzymes 9117-9121